Posted
by
timothy
on Friday October 13, 2006 @05:11AM
from the prizes-for-possibilities dept.

Shipud writes "The X-Prize foundation has announced the $10 million Archon X PRIZE for Genomics — for the first privately financed group to sequence 100 human genomes in 10 days. The motivation is to create an incentive for faster, cheaper genome seqeunceing, heralding the era of preventative personalized medicine. The winner will also receive an extra $1,000,000 for sequencing the genomes of 100 additional people; among them Larry King and Stephen Hawking. Apparently this is the largest medical prize in history."

Good. Because last time the discussion was a disgrace. Let's hope this one will be better. I'm sorry for this off-topic rant but the state of slashdot is really bugging me.I just read the last discussion. Two of the three score:5 comments were jokes. They weren't even very funny. First one was about Steve Ballmer and his chair throwing as if that thing isn't a cliche. The second one was obvious. It was about XXX-Price and "genetic material". You can figure the rest. It was pretty well writen. Hence, it was,

The IT types are not scientists. Most of them work tech support, some work in data centers, many are consultants. Comparatively few work as engineers in software or hardware. Fewer work at the bleeding edge of their fields.

Slashdot's target audience is, as a whole, uneducated with respect to molecular biology, genetics, and soforth. Most are pretty good with mathematics, but throw some advanced genetics at them and they will get lost in a hurry. It's just the way this site is.

This was already covered, but new news I found about the X Prize Cup got rejected yesterday.:(
Isn't a discussion about the new events at this year's exhibition worthwhile? Oh well.
http://www.xprizecup.com/ [xprizecup.com]

I was thinking the same thing the moment I read the headline. How long before such a device fits the size/profile of an inkjet printer? You just know potential employers and health insurance agencies will absolutely SWOON over such a product!

Do we have laws in place for genetic discrimination? If not, we should.

I don't know about the rest of Slashdot, but I don't recall the option of picking out my genetics prior to conception.

There are laws against racial discrimination that could, with a good judge that is using his/her head, would also apply in this sort of situation as well in most cases. There certainly are racial characteristics that are mapped in DNA sequences. In fact, when DNA "profiling" is used for matching up parents with kids and in forensic evidence for like a police investigation, they specifically target those DNA sequences which are not related directly to specific racial profiles, but there isn't a law that sa

The real goal here is to be able to genetically analyze people, and not what the article claims, to help them. Like any tool, it can be used for good and for bad. Like any new technology, such as aviation, or nuclear, it will probably be first tested out by the military or at least tested out in all its negative connotations before it is put to work for public good. Such people-analyzing technology will allow a new form of racism, or at least some form of historical revenge-taking. How would you like to kno

Maybe they're looking for extreme examples of the population. Hawking represents some of the best, while King represents... the other end of the spectrum.Typical Larry King interview:

Larry: Bob, did you kill your wife as the prosecution claims?Bob: (covered in blood, holding an axe still dripping from the night's first guest, whose head has been chopped into an unrecognizable blob) No, Larry, of course not. I could never hurt a fly.Larry: There you have it, folks!

100 human genomes within 10 days or less with an accuracy of no more than 1 error in 10,000 base pairs, with sequences accurately covering at least 98% of the genome, and at a demonstrated cost of no more than $10,000 per genome.

An intresting detail:

During each X PRIZE competition test, a TEAM must use its device to sequence within 10 days 100 human dip-loid genomes of 6 Gbp (6 giga base pairs, i.e., six billion pairs of DNA base molecules) each.

Note that Human Genome Project mapped and sequenced only some 3Gbp. And that was considered to be whole genome. Basically X-Price want winner to sequence all 46 cromosomes. This sounds quite difficult as the method have to be sure that is has sequenced both of the cromosomes (from a pair), not just the other one twice. And this must be valid all the 3Gbp. By bet? The working method just sequences emultiple chromosomes and determines the exact basepairs statically.

I think what's more interesting is that they want the sequences to be 98% accurate, but according to a national geographic report I found here [nationalgeographic.com] chimps and humans are only 4% different anyways. So they only want an accuracy of half the difference between people and chimps? What's the genetic similarity between Stephen Hawking and Larry King? Probably 99% or more.

With regards to this post, and the following post about 98 % coverage.The quality (i.e. the error rate) must be 0.01%, which is the convention adopted as the Bermuda Standard back when large scale sequencing was becoming mainstream, and the first genomes (of bacteria) were being produced. The coverage must be 98%. Usually, the last 2% are virtually impossible to elucidate because they are so repetitive (e.g. around centromeres) that you cannot tell how many copies of the repeats there are. The repeat regi

An intresting detail:
During each X PRIZE competition test, a TEAM must use its device to sequence within 10 days 100 human dip-
loid genomes of 6 Gbp (6 giga base pairs, i.e., six billion pairs of DNA base molecules) each.

Note that Human Genome Project mapped and sequenced only some 3Gbp. And that was considered to be whole genome. Basically X-Price want winner to sequence all 46 cromosomes. This sounds quite difficult as the method have to be sure that is has sequenced both of the cromosomes (f

I wondered about this before but I think I have it. In section 1.5, there is a limit of $10,000 cost per genome on average. In section 1.21, they state that they will pay a fee at actual cost per genome determined by the judge (nb this presumably may actually be less that $10,000). Hence, a maximum of $1,000,000.It also seems that if you refuse the 'bonus', you may be penalize by twice that amount from the initial prize.

My cash is on CodonDevices. George Church has an incredible new sequencing technology, and he's making it open source. I know some of the peeps there writing software, and between the tech and the IT team, they'll be able to generate and handle the data - the big sequencing companies ought to be scared...

Too bad the sequencing research these days is not so much focusing on fast sequencing (though that is of course still a major concern), as it is on accurate sequencing. One of the problems bio-folk are encountering is that the human genome is relatively easy to sequence: you can get all your DNA from one individual (so you only need to worry about getting two unique DNA sequences getting mixed up in the final result, one from the male and female parents) and there isn't as much repetition as compared to say

any true revolutions at a company or other entity that allows this level of an improvement over current sequencing tech will have so much VC money (or parent company cash) rolling in that $10 million won't even be worth the time for application. Then when the tech is validated and ready for use, they wouldn't have time to cash the check for $10 million while the billions are rolling in.

For those of you in other fields, imagine in the next jet propulsion X prize was $10 million to the first group to come up with a working drive capable of 20% of the speed of light within a day of ignition. Or how about a single computer CPU capable of processing 100 peta flops. Or a system capable of cracking a gallon of water but using only 100 joules of electricity.

Sure, some day these may all be possible, but right now they are pie in the sky at best.

Can someone explain what genome sequencing actually does? Does it "simply" give you a complete description of the base pairs of someone's DNA?
Yes. Actually, even less than that. "Shotgun" sequencing give you a collection of random seqeunces of base pairs, ~1,000 BP long. You need quite a few of those to reassmeble the human genome, computationally.
Or is it a little more complicated than that, telling you where the individual genes begin and end? What information can you derive when you know the sequ